Okay I have a fix for this issue. Update: Pro version only.
Cart66 changed the way the pop up box worked to "give" developers more control over when it loads the js that is need to display the pop up boxes content.
What I find clumsy is that the button that calls the pop up is still there.
What I find clumsy and irritating is that they felt that they need to do this in the first place.
Why not add a hook that lets you turn off the pop up if thats what you want.
This is how you use the new cart66_add_popup_screens filter :
// using cart66 filter: cart66_add_popup_screens
// first we need to add the filter
// because cart66 only applies the filter, it does not add it.
$array = array('products','plugins'); // this is a list of the custom post types